Spatial Cross-Talk between Oxidative Stress and DNA Replication in Human Fibroblasts

Abstract

MS-based proteomics has been applied to a differential network analysis of the nuclear-cytoplasmic subcellular distribution of proteins between cell-cycle arrest: (a) at the origin activation checkpoint for DNA replication, or (b) in response to oxidative stress. Significant changes were identified for 401 proteins. Cellular response combines changes in trafficking and in total abundance to vary the local compartmental abundances that are the basis of cellular response. Appreciable changes for both perturbations were observed for 245 proteins, but cross-talk between oxidative stress and DNA replication is dominated by 49 proteins that show strong changes for both. Many nuclear processes are influenced by a spatial switch involving the proteins {KPNA2, KPNB1, PCNA, PTMA, SET} and heme/iron proteins HMOX1 and FTH1. Dynamic spatial distribution data are presented for proteins involved in caveolae, extracellular matrix remodelling, TGFβ signaling, IGF pathways, emerin complexes, mitochondrial protein import complexes, spliceosomes, proteasomes, and so on. The data indicate that for spatially heterogeneous cells cross-compartmental communication is integral to their system biology, that coordinated spatial redistribution for crucial protein networks underlies many functional changes, and that information on dynamic spatial redistribution of proteins is essential to obtain comprehensive pictures of cellular function. We describe how spatial data of the type presented here can provide priorities for further investigation of crucial features of high-level spatial coordination across cells. We suggest that the present data are related to increasing indications that much of subcellular protein transport is constitutive and that perturbation of these constitutive transport processes may be related to cancer and other diseases. A quantitative, spatially resolved nucleus-cytoplasm interaction network is provided for further investigations.

Spatial perspectives in the redox code—Mass spectrometric proteomics studies of moonlighting proteins

“…Black: responses based on inborn metabolic errors, adapted from Olsen, Cornelius, & Gregersen (). Green: additional responses identified in recent MS‐based proteomics studies (Radulovic et al, ).…”

Moonlighting Proteins and Cardiopathy in the Spatial Response of MCF‐7 Breast Cancer Cells to Tamoxifen

“…Their response to Tam was measured for total change in protein abundance and for compartmental changes in protein abundance in the nuclear and “cytoplasmic” (nucleus‐depleted) compartments . The purity of the nuclear/cytoplasmic fractions obtained with the subcellular fractionation protocol previously optimized were routinely tested using western blotting . Stringent purification of organelles (e.g., nucleus) was not attempted since stringent organelle isolation procedures can lead to loss of ability to monitor important characteristics of dynamic cellular function.…”

“…Stringent purification of organelles (e.g., nucleus) was not attempted since stringent organelle isolation procedures can lead to loss of ability to monitor important characteristics of dynamic cellular function. We preserved the ability to study dynamic features by using differential isotope labeling of cells with/without exposure to Tam and subcellular protocols during data analysis …”

“…We have developed high‐throughput proteomics methods suitable for investigating dynamic aspects of protein subcellular distribution in the response of cells to stimulations . This approach, which combines global quantitative proteomics with the analysis of fractions enriched in target subcellular locations, has allowed measurement of the changes in total abundance and in the compartmental abundance/distribution between the nucleus and cytoplasm for several thousand proteins differentially expressed in MCF‐7 cells in response to estrogen stimulation.…”

Effect of Inulin on Proteome Changes Induced by Pathogenic Lipopolysaccharide in Human Colon

“…In the present study, we also observed an increased content of the CCT subunit eta (CCT7) in LPS+INU treated samples compared to the control. CCT orchestrates the folding of many newly synthesized proteins and it is involved in membrane fusion events [31, 32]. Moreover, it seems to be important in the retrograde mitochondria signaling induced when mitochondria antioxidant defenses are overwhelmed.…”